We start the episode with this chilling warning. See, this is why the pilot episode is, in this case, one of my favorite episodes. As we know, the first episode usually isn’t that great, and this episode definitely isn’t perfect, but wow. The eerie factor is there without being overly cheesy.

We’re given just enough time to consider the implications of that warning before being thrown into the episode, and what we see doesn’t help the unsettling feeling in our stomachs. A girl running through the forest. Wind and strange lights. A mysterious figure.
The next day, the girl is found dead and a police officer asks someone, “It’s happening again, isn’t it?”

At FBI Headquarters. Dana Scully arrives at Division Chief Scott Blevin’s office. They have a brief interview that gives us a general idea of her backstory. We find out that she was going to medical school but joined the FBI instead of becoming a doctor because she wanted to distinguish herself.

A man sits in the corner throughout the entire conversation, silently smoking a cigarette. This is our first look at the infamous Cigarette Smoking Man. Keep an eye out for him.

Blevin tells Scully that she is going to start working with Fox Mulder and The X-Files. Her goal, essentially, is to play along with Mulder but also write reports, debunking the mysterious files with science.

Our beloved children, who have only just met and have no ideas what adventures lay before them, discuss their first case - a young female, Karen Swenson, was found dead with strange marks in her back, which Mulder believes are of alien origin. Scully is classically skeptical. However, three of her classmates have also died under mysterious circumstances.

“Do you have a theory?” - Scully
“I have plenty of theories.” - Mulder

They fly to Oregon. Scully reads over the case while Mulder naps, and he continues napping while the plane begins shaking violently in an abnormal and frightening manner right before their descent. It’s definitely weird, but Mulder is unfazed, if not mildly smug, over the incident. He remains unfazed yet mildly smug when, while driving to meet the local Coroner, the radio randomly turns on and they hear strange, high pitched noises. Mulder stops the car at this point and marks a red “X” on the road with spray paint.

Once this incident is over, they head to a graveyard, where the Coroner and his assistant are waiting so they can exhume the body of Ray Soames, one of the three teenagers who died under mysterious circumstances, and also Karen Swenson’s classmates. They are rudely interrupted by a Doctor Nemman, who conducted the autopsies on all of the young adults that died...except for Karen, because, as he explains, he was out of town. Eventually he leaves, his daughter persuading him to go, and the agents and coroner resume their investigation. Here’s where things get weird. Ray Soames body appears to have been replaced with a strange, dare I say alien-like, shriveled up corpse. An autopsy reveals a small metal piece in the body's nose.

From here, Mulder and Scully decide to visit two of the living classmates - Peggy O’Dell and Billy Miles. They’ve been hospitalized for four years, and we find out that Ray had been hospitalized too for a year before he died. Unfortunately, the agents find Billy in what is referred to as a “waking coma” as a result of a car accident. Peggy was also in the car accident, and it left her in a wheelchair. She refuses to talk to Mulder and quickly becomes agitated. She begins having a nosebleed and falls - or throws herself - out of her wheelchair. As Mulder helps get Peggy back into her chair, he notices two marks on her back...just like what Karen had.

Realizing that all of the strangeness surrounding the deaths and the accident that Billy and Peggy were in happened near the woods, Mulder and Scully decide to go check out the location. They are stopped, however, by a man clearly involved with the law enforcement. He demands they leave the woods, claiming that it’s private property.

So, they drive back to the motel. Scully shows Mulder a handful of dirt that she pocketed and suggests that the kids might have gotten involved in a cult. Mulder is distracted and glances down at his watch. Suddenly, there is a blinding flash of light, and the car stops. Mulder realizes, looking at his watch again, that what seemed like only a matter of a couple of seconds was actually nine minutes. He’s thrilled over this “lost time,” while Scully is in shock and insists that this couldn’t have happened because time is a constant throughout the universe.

They finally get back to the motel, and things continue to grow stranger. The power goes out, and Scully goes to take a shower by candlelight to try and calm herself down...only to discover strange marks on her back. Mulder examines them and assures her that they are only bug bites, but it’s a heart-stopping moment anyway. I have to point out that I love that they had the power go out in this scene - having everything happen during a thunderstorm and by candlelight adds a whole other element of “creep” to the entire scene.

It is, of course, while we are still mildly spooked out from what just happened that Mulder shares some of his backstory with Scully. According to Mulder, his sister Samantha was abducted when he was 12. He says that he’s gone through regression hypnosis with Dr. Heitz Werber, and what he remembers led him to believe that Samantha was was kidnapped by aliens, which in turn seems to fuel his fascination with the X-Files. While he does say that he has “connections in Congress” that allow him to continue his work researching the X-Files, he knows that there are people in the government who want to stop his and accuses Scully of being part of their agenda. She denies this.

They receive a phone call where an anonymous woman tells Scully that Peggy O’Dell, the wheelchair bound girl in the hospital, is dead. The agents rush to the scene and find out that she was hit by a car. The driver tells them that she ran in front of the car, which is definitely strange considering that she supposedly couldn’t walk anymore. Scully examines the body and sees that Peggy’s watch stopped at the same time she and Mulder experienced the time loss. Mulder finds out that the lab where they had performed the autopsy on the strange body has been trashed and the body is missing. They return to the motel to find their rooms up in flames, all of the evidence gone except for the mysterious metal piece that Scully had found in the body’s nose. Fortunately, she had tucked it into her pocket before they left.

A young woman rushes over to the agents and asks for their protection. She is Theresa Nemman, the daughter of the doctor that performed the autopsies on the other dead teenagers. She is also the anonymous woman who made the call to tell them about Peggy. They take her to a diner, and she shares that her dad is indeed hiding things and that she has the same spots as the other teenagers. Her nose starts to bleed right before her dad and the same law enforcement officer that told Mulder and Scully to leave the forest enter the diner. They find out that the officer is Detective Miles....Billy’s dad.

Doctor Nemman insists on taking his daughter home, and the agents are unable to stop him. So Mulder and Scully decide to go to the graveyard, where they discover that the other two bodies have already been exhumed. Mulder has a revelation and reveals that he believes Billy Miles is the killer.

According to Mulder, all of the strange events seem to fit the profile for an alien abduction, especially the fact that Peggy was killed at the same time that the agents lost nine minutes. He says that he has a theory that the aliens were doing experiments on the kids, which explains the marks on their backs, but that it caused a genetic mutation, explaining the disfigured corpse of Ray Soames. He goes on to explain that he believes the aliens could have taken control of time itself and Billy, making him go to the forest and kill the other victims.

So the next day they visit Billy. The nurse insists that Billy has never left the hospital, but the dirt on his feet seems to prove otherwise. Unfortunately, while Scully theorizes that this is the same dirt that she found in the forest before, that sample of dirt is now gone thanks to her motel room catching on fire. They head back to the forest to get another sample, but when they get there, not only do they see Detective Mile’s car, but they also hear a frightened scream in the forest.

They run towards the direction of the scream, but Scully is knocked over by Detective Miles, who says he warned her to stay away. He then catches up to Mulder and holds him at gunpoint, but Mulder accuses him of knowing everything and tells him that his son is about to kill another person. They find Billy with an unconscious Theresa in his arms. Mulder wrestles the gun away from Detective Miles and fires it into the air, alerting Scully. Billy lifts Theresa towards a blinding light, which envelops everyone standing nearby. Scully watches from a distance.

Back at FBI headquarters, Billy goes through regression hypnosis with Dr. Werber while Blevins, Scully, and The Cigarette Smoking Man watch. He shares what he can remember from the alien abduction and admits that he’s afraid they’ll come back. Later, in Blevins office, he asks Scully about the case and whether she believes it or not. She seems to believe Mulder but is also hesitate to admit it. She gives them the metal nose piece and leaves. We see The Cigarette Smoking Man take the piece down to a secret room full of files and boxes. He stores the piece with other similar looking metal pieces and leaves.